<HTML><BODY><p>Dear David!<br><br>Option -dr, it is new?<br>Perhaps, you meant - dt? There is no wish to thin out a trajectory.<br>Sincerely,<br>Boris.</p><br><blockquote style="border-left:1px solid #0857A6; margin:10px; padding:0 0 0 10px;">
Суббота, 4 августа 2018, 16:09 +03:00 от David van der Spoel <spoel@xray.bmc.uu.se>:<br>
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<div id="style_15333881610000000136_BODY">Den 2018-07-26 kl. 14:02, skrev Boris Timofeev:<br>
> Dear developers!<br>
> <br>
> The existing realization of "gmx cluster" for calculations uses <br>
> RMSD-matrix,<br>
> quadratically increasing with increase in length of a trajectory,<br>
> and already since 20000 frames calculation of clusters becomes impossible<br>
> because of requirements to memory and time.<br>
> <br>
> Whether there are some special methods for a clustering of trajectories <br>
> of big duration,<br>
> containing 100000 and more frames?<br>
Use the -dr flag.<br>
> <br>
> Best wishes<br>
> Boris Timofeev.<br>
> <br>
> <br>
> <br>
> <br>
> <br>
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-- <br>
David van der Spoel, Ph.D., Professor of Biology<br>
Head of Department, Cell & Molecular Biology, Uppsala University.<br>
Box 596, SE-75124 Uppsala, Sweden. Phone: <span class="js-phone-number">+46184714205</span>.<br>
<a href="http://www.icm.uu.se" target="_blank">http://www.icm.uu.se</a><br>
-- <br>
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<br>-- <br>Boris Timofeev<br></BODY></HTML>